Document summary

This document has been generated for paper (Differential expression, co-expression and functional analysis of RNA-seq data using the DEgenes Hunter suite and its applicability to rare disease):

Measures are calculated with following formulas:

  • Accuracy (ACC): \(\frac{TP+TN}{TP+TN+FP+FN}\)
  • Precission (PPV): \(\frac{TP}{TP+FP}\)
  • Recall: \(\frac{TP}{TP + FN}\)
  • Specificity: \(\frac{TN}{TN + FP}\)
  • F-Measure: \(2*\frac{Precision * Recall}{Precision + Recall}\)

Synthetic results summary

Source table with all results is shown with a set of graphics which check the effect, over the AUC of each package, of each configured parameter. Note: samples are mixed in graphs which are not x.axis=Sample.

Also, a sumamry of all datasets are compared bellow fixing the number of genes to minimum and number of replicates to minimum, showing a grid with samples (rows) and DEG proportions (columns) and a plot of AUC obtained (y-axis) depending on the maximum fold-change simulated (x-axis) and grouping by package results (colors):

Finally, a comparisson between Vote and Combined systems is shown using different measures (rows) into each sample (columns), also two dashed lines have been added at mean of combined and largest cut of both systems:

Sample Arabidopsis

Results for especific sample (Arabidopsis).

Summary for this sample:

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Extended study : Arabidopsis

Per each configuration, a plot of AUC (y) grouped by maximum logFC to simulate (x) will be plotted, grouping by number of genes (rows) and DEG proportion (columns) simulated:

Vote systems results : Arabidopsis

Measures (y) comparisson for all possible vote systems thresholds (x) grouping by number of replicates (columns) and each configuration (grid set):

Sample Lafora

Results for especific sample (Lafora).

Summary for this sample:

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Extended study : Lafora

Per each configuration, a plot of AUC (y) grouped by maximum logFC to simulate (x) will be plotted, grouping by number of genes (rows) and DEG proportion (columns) simulated:

Vote systems results : Lafora

Measures (y) comparisson for all possible vote systems thresholds (x) grouping by number of replicates (columns) and each configuration (grid set):

Sample PMM2

Results for especific sample (PMM2).

Summary for this sample:

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## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html

Extended study : PMM2

Per each configuration, a plot of AUC (y) grouped by maximum logFC to simulate (x) will be plotted, grouping by number of genes (rows) and DEG proportion (columns) simulated:

Vote systems results : PMM2

Measures (y) comparisson for all possible vote systems thresholds (x) grouping by number of replicates (columns) and each configuration (grid set):